For a superintegrable system defined in plane polar-like coordinates introduced by Szumiński et al. and studied by Fordy, we show that the system with a position-dependent mass is separable in three distinct coordinate systems. The corresponding separation equations and additional integrals of motion are derived explicitly. The closure algebra of integrals is deduced. We also make a generalization of this system by employing the classical Jacobi method. Lastly a sufficient condition which ensures flatness of the underlying space is derived via explicit calculation.